Fallen Heroes: Book One Version 2
by SeanKR
Summary: The Survivors of the Twelve Colonies of Kobol are searching for what they believe is the long lost thirteenth tribe on a planet known as Earth. The first clues on their journey are found on the long lost mother planet for them Kobol. Heading into an area of space where they believe they will find Earth and hopefully sanctuary and a new start while on the run still from the Cylons.
1. Chapter 1

**This story is written with the permission of thefallensith, and is a relaunch of and inspired by his story "Fallen Heroes". I do not own anything within this story save for any characters I create for its use. BTW I am totally Ignoring Stargate Universe and most of the related material from the story (as most SG fans have) but I do reserve the right to have some characters from SGU possibly make cameo appearances in my story if I feel they fit the storyline or I like the character. Both Stargate and Battlestar Galactica 2003 belong to their perspective companies and or production firms. As always opinions and ideas are welcomed, please keep any and all flames to a minimum.**

Summary

The Survivors of the Twelve Colonies of Kobol are searching for what they believe is the long lost thirteenth tribe on a planet known as Earth. The first clues on their journey are found on the long lost mother planet for them Kobol. Heading into an area of space where they believe they will find Earth and hopefully sanctuary and a new start while on the run still from the Cylons. However what if rather than finding Earth, sanctuary, and a new beginning. They instead find survivors from Earth attempting to regroup after losing their world to an Enemy far greater than the Colonies have ever seen. An enemy who will test the mettle of not only the survivors of the Colonies and Earth, but the Cylons as well.

**Fallen Heroes: Book One**

**Chapter One**

March 1, 2013

Samantha Carter-O'Neill, Territorial Governor of Atlantis stood on the balcony outside her office looking out at the grey sea, leading to a grey sky on alien world watching the sunset thinking to herself what was wrong with her. Here she was with a little over two million evacuees on Atlantis alone, and she is not thinking of the more than six billion people they had to leave behind on Earth. Nor is she thinking of the lives lost in the burgeoning fleet of 304's and 303's that attempted to stop the Wraith Invasion Fleet outside of their galaxy but failed miserably, only slowing the Wraith down rather than stopping them. No she is not thinking of any of that instead she has only one thought going through her mind right now, Jack O'Neill.

She and Jack O'Neill had been through more together than any other couple she had ever known, possibly any other couple in history. That all culminated for Sam seven months ago after her last tour of duty on the Hammond and her subsequent promotion to Brigadier General. She had been called to the White House to meet with the President of the United States. Now despite the fact that Sam Carter at the time had faced down system lords, evil robots, a demented robot clone of herself, and ascended beings that could quite conceivably and did in fact pass themselves off for gods, she was a bit nervous about meeting her Commander and Chief as well as leader of the free world in person. The meeting however went very well, what surprised her though was not how the President seemed a little star struck with her. What surprised Sam was the fact that the joint chiefs and Jack O'Neill were there.

They chatted for several minutes before the President than went into the reason he had called for her, Atlantis. Apparently between having the SGC, Area 51 Research and Development, as well as the Expanded 303 (both a Light Carrier version called the Lexington sub class and Cruiser variant called the Des Moines sub class of the 303) as well as the 302 C & D program being run by the Navy all moved in there over the past four years since it's return to Earth. All of these things had culminated into making Atlantis become a logistical and administrative nightmare. One that even the I.O.A., in their supposed infinite wisdom, could not even handle. It was in fact Dr. Daniel Jackson, who came up with a plausible solution to the situation. Atlantis would become an independent city state, apparently there were enough people on the City Ship currently to justify doing so. The five leaders in the I.O.A. treaty nations could than appoint someone to act as a Territorial Governor of Atlantis until a more permanent solution could be agreed upon. Of course the other leaders had their own ideas about who should be the interim Governor but few if any could agree on a single person. Until the President mentioned General Carter. Than the other leaders seemed to agree with Russia abstaining, and China of course dissenting but having already agreed to go along with the majority decision in all off world or Stargate matters and technology, abides by the majority decision.

Sam took all of two seconds to decide to agree, but waited several minutes before she had voiced it. She remembered how the next day she was at Cheyenne Mountain, in what was to become the Old SGC clearing out her office. When Jack O'Neill walked in, just checking the old place out he had said. They chatted about non consequential stuff for several minutes until to Sam at least out of the blue, Jack with some effort got down on one knee, and proposed to her. This time when Sam was silent for several minutes it was not because she was making Jack suffer, she was simply in a state of shock, that plus the two carat diamond ring Jack was presenting to her was quite simply beautiful. They were married three months latter (it would've been sooner but Sam insisted on Teal'c giving her away) on Atlantis. The hardest part was not the wedding or even arranging for all those invited to be on world at the time. No the hardest part was getting someone cleared to officiate over the wedding on Atlantis.

Three months of wedded bliss was all Sam had, before the Wraith fleet came. The last time she saw Jack was when they were both in The Homeworld Command bunker in the Pentagon. They had just received word of the fleets attempt to stop the Wraith, they Failed! Of the seven DSC 304's sent only three were returning and 2 were damaged as were four of the twenty 303's. Somehow the Wraith had not only upgraded their hyperdrives but these hives's had shield's. Of the six hive's detected one was destroyed and two were damaged but not majorly. When the report can in from the Odyssey of the battle Sam was standing next to Jack she turned her head and saw the look in his face. Rather than acknowledge her though he simply handed her a sealed envelope with the seal of the President of the United States on it, squeezed her hand and told her simply "Save whoever and however many you can." He then kissed her goodbye, and contacted the Exeter and ordered them to transport her to Atlantis. After that she was engulfed in a transporter beam and found herself in Atlantis where she immediately went into command mode and began issuing orders. Two days later Atlantis left Earth again surrounded by the three of the five remaining DSC 304's and sixteen of the remaining twenty 303's (the other 304's and 303's being locked down on Atlantis' docks for latter repairs). Every vessel and Atlantis itself was filled to capacity with supplies and what people they could save from the Earth.

They latter learned the Jack O'Neill had gone on to the SGC itself to oversee the continuing evacuation of Earth via the Stargate to their five off world Milky Way bases. The last people through the gate (who had left Earth nearly twenty four hours after Atlantis had left) confirmed that at the time they left O'Neill had still been alive. However they also stated that he had left the control room to take command of the last line of defense as the Wraith were invading the SGC. It was within hours of their arrival at the Delta site that all communications with Earth had been lost. No attempts had been made by any off world site to connect to Earth via the Stargate nor would there be any. Earth, as far as anyone was concerned, was a quarantined planet.

Sam was brought out off her reverie by a knock on her office doorframe. She heads back into her office and see's Atlantis's military commander, Colonel John Sheppard, standing there. She smiles waves him into the office as she heads to her desk.

"What have you got John?" she asks as she sits down.

"Didn't mean to disturb you so late," John begins moving into the office taking a seat in one of the chairs in front of her desk, "but I've got that information you requested, and some updates on ship's status."

Sam activated her enhanced laptop as John activated his enhanced tablet. Both devices looked like your standard over the counter systems however they had both been enhanced by computer technologies the SGC had discovered and reverse engineered over the years.

"Alright," John started "first things first, population, when we left Earth, we had rescued and had onboard Atlantis a Grand total of 2,185,275 people. This includes the SGC/Atlantis staff and teams as well as Area 51 researchers and ship yards personnel which came to approximately 125,275 people. I am not including the families of those people who were also picked up."

Samantha nods at that in understanding, "So where do we stand now?" she asks.

John sighs," Well, as you can imagine some people haven't dealt with the shock too well. In fact Carson and Jennifer are working with several psychotherapist's and psychiatrist's as well as priest's and any clergyman & women to help with the depression issues that we are seeing however..." John paused.

Sam could see he was upset about something and asked "Is it that bad John?"

"We've had close to fifteen thousand cases of suicide since we left Earth last month." John finally blurted out.

Sam placed her face in her hands and struggled with her emotions for several minutes before she looked back up at John Sheppard and asked. "How, and what are we doing to slow it down or stop it."

John just looked at her seeing her regain control he continued. "Most of them occurred within the first two weeks. Groups of people just walked out to the piers and jumped off after we left Earth, according to Rodney and Zelenka most of them hit the shield at near relativistic speeds those who didn't slid down the shield bubble and were incinerated in Atlantis's engine wash. Apparently some even did it when we were in hyperspace," sighing "the rest were people who jumped from their balconies in whatever building they were placed in. As for what we are doing, I mentioned the psychotherapist's and psychiatrist's as well as the priest's and clergy, for the time being access to the piers is restricted to an as needed basis, I've also got MP's & SF's doing regular patrols with stunners, or intar rounds looking for any problems, and any docked 303 that is able is performing constant scans of the city looking out for any jumper. If one is found their transported to either the 303's brig or Atlantis's until they can be evaluated, treated, than hopefully returned to the general population."

Sam looked at John as she took all of the information in before she formulated her response. After a moment or two she replied, "Make sure the psychiatrist's and the psychotherapist's keep Carson and Jennifer in the loop with those being treated for attempted suicide we can't afford to lose too many more people." Pausing for a moment to compose her thoughts Sam continues," I'm not very comfortable with MP's & SF's performing regular police work so we need to get a solution for that quickly."

"Already ahead of you, "John replied "according to our census report we picked up about 1500 regular police officers from about 5 different countries. The three highest ranking ones appear to be a Regional Director from the F.B.I, a Chief Inspector from Scotland Yard as well as an Inspector from Hong Kong."

"O.K. that gives me something to work with. Give me a second," Sam then touches the ear bud in her right ear and continues "Control, get me Richard Woolsey please." After a minute or two she starts talking again.

"Richard, can you come to my office?"

"I have John here, and I need to go over something's that I need the both of you to take care of tomorrow."

"Absolutely bring her with you. See you in a few minutes."

Several minutes latter Richard Woolsey walked into The Governor's office followed closely by Shen Xiaoyi. "Governor." both Richard and Shen say at the same time, as Sam waves the over to the other empty chairs in her office.

"Richard, Shen, thanks for coming have a seat." Sam say's. "John was just sharing some information with me, and I want him to tell you what he told me, and then I'll tell you what I'd like the three of you to do tomorrow." Sam then nodded to John for him to relate to them what he had just told her earlier.

After reiterating the information to them including some of Sam's comments Richard is the first person to speak. He quickly agrees with Sam about the M.P's and S.F's and also agrees that they need to get the regular police back to doing their jobs as soon as possible. He then mentions that it is probably why both he and Shen where asked into the meeting. Sam confirms and gives Richard, Shen & John the rundown of what it is she wants' them to do. Richard and Shen are to work with the three high ranking officers and see if they can get the other police officers together to restart some type of police force working.

Whether it's a sheriff's department, marshals or a traditional police force they are to work with them to get it going. John is to help them by getting a headquarters set up for them, as well as making sure any officers joining the force receive the required training on the Zat's, Stunner's and Intar's. While there is not much difference between them and a nine millimeter there is a difference, and Sam wants them to be aware of the difference before they get into a life and death situation. Sam then turns back to Richard and Shen and informs them to mention to the senior officers that whoever will be in charge will have to answer to her and whomever she puts into whatever position will be above them depending on whatever type of Government they come up with. She then mutters just loud enough for everyone to hear that she hopes it is soon because the back log of work for her is really starting to build. In that moment Richard, John and Shen can see the weariness that has been building exponentially in Sam since they left Earth.

At Sam's mentioning of forming a government Richard informs her of several lawyers and judges just a few levels below them meeting in one of the conference rooms trying to put together a constitution for Atlantis. As well as coming up with a general bill of rights, Sam asks Richard to keep abreast of their work, and to let them know she is more interested that they get it right first and foremost rather than quickly. She mentions that if the lawyers need any guidelines to give them limited access to the database as before Atlantis had left Earth they had copied every database on the planet and stored it in the city's mainframe.

Richard and Shen were both nodding and taking notes in their own tablets as she was giving them their instructions. After Sam had finished Richard and Shen shared a look almost silently communicating with each other before Richard relayed some additional info to Sam that she really would not want to hear. Apparently along with the civilians and the family members of most of the Atlantis personnel at the time, there were some twenty five local and low level politicians whom were also aboard Atlantis. Most of them were the equivalent of a county or city council person with one who was an alderman.

At that Sam pinched the bridge of her nose moaning and mumbled barley loud enough for the others to hear how she hated politicians. She was in fact so wrapped up in that thought that she almost missed John mentioning a recent status update they received from Pegasus base that was relayed through Midway Station II. Apparently according to the update from Col. Young they were three personnel heavy at the base. The personnel in question being Senator Alan Armstrong and his family who had apparently been making the rounds of all the SGC's off world bases as he was on the Senate SGC oversight committee for the United States and was at Pegasus base when the Wraith Attacked Earth. Inwardly Sam cursed that omnipotent entity that was surly the bane of Earth and the SGC at times Murphy. The moment she did so, she realized from whom she picked that up from, Jack.

That of course brought her around to her melancholy mood from before John showed up which of course brought back her feelings of missing Jack once again. This had the effect of making Sam miss the majority of the discussion that had arisen after John had announced that Senator Armstrong and his family was alive at Pegasus Base. Richard and Shen were arguing against bringing the Senator and his family to Atlantis as they were concerned that he may attempt to make a power play to wrest control of Atlantis from Governor Carter-O'Neill. Whereas John was asserting any such attempt would fail as the Military contingent of Atlantis including the Crews of the ships were firmly behind Sam.

As soon as the argument began getting circular Sam simply ended it by shouting "**ENOUGH!**" she paused and sighed, "This arguing about Senator Armstrong is pointless and unnecessary. He can't gate to us as of yet as the macro from Midway hasn't been adjusted to send people to Atlantis rather than Earth, and it won't be for a while as we have other priorities. And I am not dispatching a single ship to the Pegasus Galaxy just to pick up the Senator and his family." She reached into a drawer in her desk and pulled out two small boxes as she stood up and moved to the front of her desk where she continued. "As far as any attempt from the Senator to take over, let's just say I have an ace in the hole, in fact Richard."

"Yes, Governor?" Woolsey replied realizing Sam was in Commander mode.

"I need you to have the senior representative from the Layers and Judges meet with me preferably tomorrow morning, before they get together to work on the constitution." Sam stated matter of factly before turning to John." And I'll have no more talk from you or any other military personnel about ANY type of military coup!" She them gave him a stare that he had heard about from Jackson and O'Neill and had only seen once before when she chewed out Col Ellis for his treatment of McKay during the planning stages of the assault on the Asurans. "Do I make myself clear Colonel!"

"Yes, Governor" John said "perfectly clear, I'll spread the word A.S.A.P."

"Good, now I believe you had some things to report on John?" Sam asked as she crossed her arms and leaned against her desk.

"Right, first things first," John paused looking at his tablet before continuing, "Ships Status. According to McKay, the Daedalus will take another three weeks to repair, the Hull damage from the wraith hit on the main bridge after her shields failed is repaired. However when the C.I.C. section overrode the bridge controls to evacuate the battle, according to McKay they botched the override and fried every control crystal on the ship. He's still chewing out the C.I.C. crew, and making them do a majority of the work, all the while lecturing them on where they went wrong and what they should have done. What they don't know is, McKay is planning on quizzing them after the repairs are done, before they can get back on the ship." He said as a slight smile spread across his face.

"Ouch," Sam said with some sympathy for the C.I.C. crew, granted they did save the ship as well as General Caldwell's life, but having seen the after action reports and the extent of damage to the Daedalus that was Not directly related to the battle, let's just say she felt they were getting their just deserts.

"Lt. Col. Marks has assumed command of the Daedalus until we know whether or not Steven will be back to duty, any word from Jennifer or Carson BTW?"

Sam sighed she did in fact have news, "Yeah, I got word from Carson earlier today, He lost his left eye in the bridge strike, as well as nerve damage to his left arm. As you know his right leg was crushed by the support frame, they were hoping to save it. They had to amputate it earlier today."

"Damn!" was all John could say, Richard and Shen remaining respectfully silent.

"They offered to have me heal his leg with a Goa'uld hand device but...he rejected it." Sam continued, "After his possession a few years ago by a symbiot, I can't say I blame him."

They all just stayed there in silence for a few moments before Sam spoke up again. "John let Marks know that he is now the commander of the Daedalus. We'll arrange a time latter to have a promotion ceremony for him to commemorate his becoming a full Colonel."

"Right, I'll have Rodney manufacture some insignia so Marks can wear them at least."

Sam, smiled "Or you could just give him yours...General!" as she tossed one of the two boxes she pulled from her drawer to John. He caught the box easily enough but refused to open for several minutes fixing Sam with a pointed look not wanting to believe what she had just said to him. He did eventually open it though and inside was exactly what he thought was there two silver stars.

Before he could even come up with a reason why he didn't deserve this Sam leaned behind herself and typed in a command on her laptop as she did this she informed John and the others what she was doing.

"Before you object to this John, I want you to read these letters I am sending to your tablet."

John looked to his tablet, and saw the e-mail's Sam had sent to him with the files attached. There were four documents in total each one labeled, as was typical of official documents, as the date they were written. The first one was written approximately eight months ago, clicking on the icon John opened it and begins reading it. Immediately he felt shocked by the contents, it was a recommendation letter written by Jonathan 'Jack' O'Neill, for him to be promoted to the rank of Brigadier General. The second letter was also a recommendation letter but was from Maj. General Hank Landry, and the third was from former President Henry Hayes. All three letters were addressed to the current President of the United States. And that was exactly who the forth letter that John opened was from. But this letter was addressed to the Congressional and Senate Defense Oversight Committees recommending Colonel John Sheppard for promotion to Brigadier General.

John spent several minutes looking over the letters from men he respected and admired. Just the letter from General O'Neill was in and of itself a shock. But the ones from General Landry and Former President Henry Hayes. It was no wonder he did not notice that Sam had moved back behind her desk until he heard her speak.

"Now General Sheppard," Sam began in a tone the John understood that she would reject his attempts at bucking the promotion. "Do you have any additional information for me?"

John snapped out of his stupor and continued his report to the Governor "Yes ma'am." He closed the letters on his tablet and pulled the reports back up for ships status.

"Alright, Rodney and the dock yards were able to get the Navies 304 the USN Excelsior, as well as her Light Carrier 303B the USN Lexington and the Cruiser 303C the USN Des Moines repaired as well as their British counterparts The HMS Ark Royal and the HMS Yorktown repaired. The 303's only suffered moderate hull damage and needed to have some of their 20MM CIWS rail guns replaced. They went ahead and replaced them with the dual barrel variant rather than the standard barrel, since it performed so well on the Odyssey. They also replaced all of their 50MM main rail guns with the new dual barrel version they have been working on as well. And Rodney came up with a way to modify the Asgard emitters so they can fire ion bolts rather than the plasma beam they normally fire from the 304's and installed them on the ship's. The Des Moines class will carry six of them and the Lexington class will carry 4."

"Wow," Sam replied in shock, "how did he do that? The 303's don't generate enough power from the mark 2X to power the Asgard weapons. And we haven't completed research on the mark 3X, and the mark4X in the 304's won't fit in the 303's "

John got a small grin on his face "In answer to the first question he hooked each emitter up to the Asgard Core, and changed the weapons settings option through that. The 304's have that option also since they have an Asgard station built into them by default. But the 303's don't. As far as power is concerned, in part that was why he hooked each emitter into the core to change their settings they can't fire the PBC but just about everything else they can which is why he also installed some of the excess vacuum batteries for the Puddle Jumpers as a dedicated power source for the emitters. Best part is we have already proven we can recharge the batteries with our naquadah reactors since that's what was recharging them when we initially came to Atlantis."

Sam had to say she was impressed using the vacuum batteries as a dedicated power source for the Asgard emitters and changing their settings to fire a different weapon then what is normally the default setting was simply a stroke of genius and she said so to Sheppard as well as, "Tell Rodney I said congratulations on the idea, it's genius."

John's grin became a full blown smile and Sam knew something was up so he told her before she could ask. "Actually, you should thank Eli Wallace, as they were both his ideas."

Sam's face scrunched up a bit as she tried and failed to put a face to the name, and failed. Fortunately John continued before she could even ask who he was.

"He's the kid who hacked the pentagon a few years back and almost got into Homeworld defense's systems, before the Asgard system kicked him out."

That kicked Sam's memory, apparently Eli's friend's came up with a stupid game of hack the government, with each successive person having to hack a more difficult system and trying to get in as deep as possible before being detected. Unfortunately for Eli by the time it was his turn only the Pentagon was left. What was his saving grace from a life in prison was the fact that he had somehow done what every analyst in Area 51 thought was impossible, he had actually hacked into the Asgard system that was Homeworld commands servers. That brought him to Jack's attention, it didn't take them to long to track the kid down. Once they did Jack went and gave the Kid two choices, work with him or go to jail. Eli decided to sign up for homeworld command, but only after Jack agreed to help his mother with her medical issues.

And now she knew why John was smiling, the fact that this might work and he hadn't thought of it would definitely burn McKay to no end.

"Make sure you don't rub Rodney's nose in it too much John." Sam said with a slight grin on her face. "Anything else?"

"Yeah on the Excelsior, Rodney went ahead and replaced all the standard rail guns with the DBRG's. He also went ahead and had their load out's increased as well. He was going to install the software Eli found for changing the Asgard emitters but it was already installed in the Asgard station so instead he just made sure it was up to date and tied it into the weapons officer station. We've gone ahead and passed that info on to the other 304's and their updating their systems as we speak. Now onto the part you might not like, Rodney went ahead and installed the M.A.C. (Mass Accelerator Cannon) we've been experimenting with onto the lower hull of the ship. He said it was perfect since the entire lower hull down the centerline of the Excelsior was nearly sheared off by the Wraith when her shields failed briefly. It's not the final version, but it'll give the Excelsior a hell of a lot more fire power than before. Right now it's set to fire the modified 150MM SABOT rounds at mach 7 with an effective range of 750 miles nominal load out is 250 rounds, that's not counting the 50 modified naquadah/potassium rounds."

"The M.A.C. was never meant to be mounted on a shipboard platform, it was designed as a planetary based defense system only. He should have known better than that. Damn him!" Sam sighs and reigns in her emotions before continuing," well it's too late to do anything about it now." Sam sighed again in resignation before she looked to Sheppard and pointing her finger continued. "You make sure McKay knows if that thing blows up in Captain Harris face either in testing or in Combat then BOTH of you are going to do ALL of the repairs personally, BY YOURSELVES!"

"Hey, why are you picking on me, it was McKay who installed the system not me?"

Sam glared at Sheppard before she continued, "Because you two are as thick as thieves despite what you may say to the contrary. There is no way McKay install's that system without running it past you first. Or at least talking to you about it. And you should've brought it to me before you had him install it."

At the accusation John began squirming in his seat before finally relenting. "Ok, geez. In the future I'll run any upgrades past you before we do them. Sorry."

Before Sam could respond though John continued, "One thing you do need to know right now though, you remember those strange subspace energy readings since Atlantis came back to the Milky Way Galaxy?"

"Yeah, we tried to send an SG team to investigate them but there were no active gates in the area at all as I recall. And anytime we tried to send a ship to investigate something else just came up. Has there been a change in the readings?"

John, looked to his pad and pulled up his notes to verify before he continued, "According to the logs, about six months ago the number of subspace distortions in the Cyrannus System increased for a day or two before dieing down to below previously recorded levels where they are still at right now." John paused rechecking his notes before continuing. "Now according to the science guy's twelve of the planets in that system now show a greater than normal radiation signature possibly indicative of nuclear bombardment but at this range we aren't absolutely certain either. However we are tracking several ships that are apparently moving away from that system we're not sure what they are looking for but they did stop off at this planetary system here for several day's before another ship showed up. They went back a few days latter and then about two to three weeks latter several ships departed the main section of their fleet and headed there. They were there for a few days before another small ship joined up with them and then they all headed back to rejoin the main fleet. They have since resumed their course away from the system and are currently about 250 light years away." John again paused waiting for Sam to respond when she did not for several minutes he continued on. "Anyway, that finishes the Major reports you requested, there are a few minor housekeeping things we need to discuss, mainly about personnel, power reserves and supplies. But their not critical and we can go over them latter if you want."

Sam looked at the clock and saw the time as being well after midnight local time, where had her day gone she thought to herself. She than looked to John, Richard and Shen and said. "Yeah let's call it a rap for tonight. John I want orders issued for the Excelsior and the four Prometheus' to go out tomorrow to test the new Asgard systems as well as the M.A.C. Have Captain Harris go to a non inhabited system to test the weapons as well as the associated systems. If they come back green I'll issue orders fore them to be installed in the other 303's A.S.A.P." Sam sighed. "Also have them do the test in a system near that fleet and have them see if they can get some readings on them but make it clear they are not to initiate contact unless absolutely necessary understood."

"Copy that." John stated than noticed the other box Sam had pulled out along with the one she had given him that contained his General Stars. Sam notices what he is staring at and tosses him the box indicating that he should open it. He does so noticing they are the silver oak leaves of a Lt. Col. he looks at her skeptically and Sam Smiles.

"They are for Lorne," Sam states matter of factly, "let him know that he is not to weasel his way out of it and have a few marines standing by just to be sure."

John nods and gets an impish smile on his face before Sam continues, "Well everyone if there is nothing else let's call it a night see you all tomorrow."

John Shen and Richard all stand up to leave saying their good nights to Sam, as she stay's in her office for several more minutes reviewing what she had accomplished and what still needed to be done. There was still so much work for her to do and more seemed to be piling on just since John came in to give his report. One request caught her eye right away, it was from Daniel and Dr. Lee about requesting some space so they could set up a school for the children they now had. She really needed to formalize some type of staff as most of everything in her pile could be regulated to them. She had some ideas of who should do what, and talking to Richard and Shen had helped to solidify at least two positions, that would give her a start at least. Again she looked at the time on her computer and decided that tomorrow would give her better answers as weariness started to seep into her. She logged off of her computer and left the office for her room her two marine guards behind her all the way. Tomorrow she would start the rebuilding process she thought, hoping she could get through the night with dreams she was certain would be dominated by one person, Jack.

**Atlantis Cityship**

**North East Dock Number 2.**

**U.S.N. Excelsior.**

**March 2, 2013 07:59 A.M.** **Local Time.**

Captain William Harris, dressed in his standard Navy service khakis rather than the flight suit analog the Air Force prefers to wear. Sat in his office near the bridge of his ship (he swore never to call it a ready room despite that is what it says on the door) going over the reports of the current status of the ships of his battle group. Among them the status of each ships repairs and upgrades, number of personnel available, and the total available supplies for the battle group. It was that particular report as well as his current orders that where taking most of his attention. The supplies report held some concern for him primarily due to a recent meeting held on Atlantis a few days ago that included all the 304 commanders as well as then Colonel, now General Sheppard and Governor Carter-O'Neill. During the meeting the supply situation for Atlantis had been brought up. While they were currently in a good situation not needing resupply for some time due to the supplies the 303's and 304's beamed from Earth as well as evacuees. Getting new supplies would be something of an issue With Earth cut off and no easy way to trade for more. Of course creating new supplies was always an option with not only the Matter Energy Convertor (M.E.C. for short absolutely NO_ONE was going to call it a replicator for obvious reasons) in the Asgard Core but also in the Asgard stations on the 304's.

Secrecy while not really a major issue anymore what with the Wraith attack on Earth and their failure to stop it essentially had let the proverbial cat was out of the bag. The question essentially became not if but when certain technological advancements should be made available to the general population. While no immediate answer was forthcoming from that meeting it did start the process and that was good in Harris's opinion.

With the supply report set aside Harris than brought up his current orders for the battle group under his command. The orders came in two parts directly from the Governor, through General Sheppard, in the first part essentially they were ordered to go to an unpopulated out of the way system and thoroughly test out the new weapons systems that had been installed on their ships during the repairs from the Wraith attack. The Governor wanted a through test of the systems on the 303's before she ordered the rest of the ships to be upgraded with them. As for the MAC installed on the Excelsior, she had given a direct order to him to thoroughly test it under as close to Combat Conditions as possible. He could've sworn he saw Gen. Sheppard flinch when she issued that order but he just dismissed it as nothing.

The second part of his orders was what brought up his concern level. He had been ordered to a very particular system for the weapons test as it was close to a fleet of ships that he was to investigate. Apparently these ships were at least in part responsible for the unusual subspace disturbances that had been tickling Atlantis's sensors for the past three years. He was ordered to look into them to determine if they posed any possible threat to their ships or to Atlantis itself. He was also ordered not to make contact unless absolutely necessary, which left that option open to his own interpretation.

Just as he was closing his orders and getting ready to log off his terminal his earpiece chirped "Bridge to Captain Harris?"

He reached up and tapped the comm. device activating it and said, "Go ahead Bridge what's up?"

"Commander Hayes here sir, sorry to disturb you Captain, but I just thought you'd like to know we just received word from the rest of the battle group as well as the dock that all personnel and supplies are onboard all ships. We are all set for up thrust and have been cleared by Atlantis control to leave for orbit at our convenience." Hayes stated.

"Very well Commander, begin the pre-launch procedures throughout the battle group. I'll be on the bridge in a minute." Harris replied and closed the channel.

He finished closing his terminal down and stood up to leave his office straightening his uniform as he left. Walking into the corridor he turned and headed towards the bridge nodding his greetings to crewman and women who greeted him as he passed. It isn't a long walk from his office to the bridge maybe five minutes at best. The designers had that in mind when they drew up the plans for the Daedalus Class.

As he walked to the doorway he noticed the hustle and bustle of activity that was going on as every station was manned as the crew was going through the pre-flight checklist in preparation for take off. He stood there watching for a moment as the officers and crewman did their duty and a small amount of pride filled him. This was his crew and his ship. He let the moment pass and walked into the bridge heading for his chair.

As he walked in the two Marine guards standing inside the doorway noticed him and the senior guard called out "Captain, on deck!"

"As you were," he replied informing everyone was to return to their duty "Status Commander?"

"Pre-flight checklist has been completed Captain, all systems are go for up thrust. Atlantis control has cleared the battle group for O.I. (Orbital Insertion) and will issue our flight path out of the nebula to our next destination once we reach O.I." Comdr. Robert Hayes said standing next to the captain's chair.

"Thank You Comdr., comms open a channel to Atlantis control please."

"Channel open now Captain." the ensign at the comms board on the port side of the bridge spoke.

"Thank you Ensign, Atlantis control this is Excelsior Actual requesting final clearance for launch do you copy over?"

After a few seconds a reply is heard by the entire bridge crew, "Excelsior actual this is Atlantis control, you are cleared for launch and up thrust to O.I. Your battle groups corridor has been cleared of all traffic. General Sheppard sends his best wishes on a good test, and requests you not scratch the paint on any of the ships, or it comes out of your pay Captain."

Harris noticed that everyone on the bridge was either slightly smiling or fighting to maintain their proper decorum on the bridge. At one point earlier in his command of the Excelsior he would have chastised the entire bridge for a breach of military protocol. But in the year and a half of his command of the ship he had learned that Stargate Command and by extension command of a Daedalus was a somewhat more relaxed command as far as Military decorum was concerned. Of course that did not mean that all military decorum was out the window so a quick look at the crew from the Captain was all it took for them to realize that the joke, while it was funny he would admit, was over. "Copy that Atlantis control; we will begin lift off procedures momentarily, Excelsior Actual out."

As he ended the conversation Harris got out of his chair and went to the back of the main bridge where his XO Comdr. Harris was having a quiet but heated discussion with someone so it would not disturb his Captains conversation. As Harris approached Hayes he finished his conversation and looked to his Captain.

"Problem I should know about Bob?" Harris asked quietly.

"Nothing I couldn't handle Captain, senior deck chief of the starboard flight pod was taking some exception to a flight of 302's that were loaded that are being covered and guarded by marines and supposedly he is not allowed to access." Hayes explained in a hushed voice.

"I take it you took care of the situation, or does he need to hear from me?" Harris asked.

Hayes looked to his Captain and long time friend and replied, "Without knowing the specifics yes sir, I informed him that if he did hold this flight up for longer than necessary I would reassign him to garbage detail and put someone else in charge of that flight deck until we got back to Atlantis." Hayes smiled "He didn't take that too kindly and relented to complaining and signed for the 302's."

Harris got a slight smile on his face before looking to his first officer seeing a questioning look in his eyes. Harris than informed him "They were a last minute addition to our flight roster by Gen. Sheppard and Gov. Carter-O'Neill." He paused before continuing "I can't really go into to much detail about them right now other than the fact that we will need them for the second part of our mission." He than looked to his friend of over twenty years making certain the underling meaning of his statement is understood.

Robert Hayes looked to his long time friend and commanding officer with a smile tugging on his lips before responding. "Aye sir, I understand. What say we get this battle group up in the air and check out these new toy's the egg heads got worked up for us?"

Harris slapped his friend on the shoulder before and said in a normal voice "Well than Comdr. Get my battle group in the air if you please" and turned to go back to his chair.

Commander Hayes smiled and said just a loudly "Aye aye Captain, All right all hands assume lift off stations and prepare to take off." He than walked up and stood beside the captain's chair. "Helm, disengage all mooring beams and make certain all outer doors are sealed."

"Aye aye sir," the helm officer replied "mooring beams disengaging, all outer doors have been sealed, engines are on standby and ready."

"All section, stations and ships report ready for takeoff Commander." reported the comms officer from the back of the bridge.

"Thank you all," the XO say's than turns to the Captain and says, "The battle group reports ready for your orders Captain."

The Captain turns to his XO "Thank you Commander, helm bring engines online and take us out," he the turns to face the comms officer, "Comms send a command to the battle group to launch."

"Aye, aye Captain." the comm. officer replied, afterwards the bridge descended into the cacophony of noises of a ship in operation. Throughout it all Capt. Harris sat in his command chair. Occasionally responding to his crew or issuing orders but for the most part allowing those under him to do their jobs automatically. Orders and commands are relayed from those stations to other sections of the ship. Within a few moments Harris hears a whine and feels his ship preparing for takeoff. Suppressing a grin he did not realize he had Capt. William Harris mentally prepared himself for his ships takeoff.

**Atlantis North East Dock Number 2**

**15 minutes earlier**

In all the years of it's operations the SGC had gained exceptionally advanced technologies as part of it's mandate to help defend the Earth and humanity originally from the threat of the Goa'uld. This of course culminated when the Asgard gifted humanity with the some total of all their knowledge and technology. Because of this one would think that manual labor jobs such as dock workers and ship builders would become obsolete. But the truth is even though they could materialize their ships completely as the Asgard could, so long has they had the power for it, humans it seems need to do things themselves, for the sense of accomplishment. Components were still materialized or in the case of the hull and frame were converted from the equivalent raw materials to a finished product.

All this meant that as the Excelsior and her escort vessels were preparing for take off there were actual dock workers and ship builders, moving equipment and supplies around the docks as well as to and from the ships. Most of what the ships were receiving was parts equipment and munitions, along with some food stocks. At least for the 303's the Excelsior herself along with all the 304's is able to construct any needed supplies from its Asgard station. But they still received some of the basic food stuffs for the crews; some things just did not taste the same no matter how well the convertors worked.

Workers were bringing boxes into the ships via hover sleds most of which had been reverse engineered from captured Goa'uld sleds from before their empire fell, as well as a few purchased from the Free Jaffa Nation. Along with the sleds are specially modified electric forklifts. These forklifts had been modified by the SGC and Area 51 to run not on a battery as a traditional forklift, but a Naquadah power cell enclosed in a block of solid steel to act as a counter balance in place of the battery. These forklifts are currently taking the shipboard missiles, and in the case of the Excelsior and the Lexington class vessels, the missiles for their flight of 302's as well.

Of course supplies aren't the only thing going into the ships, a good portion of each ships crew is returning as well. Having been reassigned to Atlantis temporarily whiles the ships where under repair and refit. A few were able to spend time with their families who had been rescued from Earth, most though were still awaiting word from the off world sites where those families that were to be evacuated would have been evacuated to. Others had taken the time to mourn their mothers, fathers, siblings, and friends. Now however was the time for them to set aside their grief and to do their duty.

Soon the stem of supplies and personnel going into the ships slows and eventually stops. What follows are the workers bringing out empty carts and forklifts leaving the vessels, sealing the doors behind them. The hover sleds and forklifts head for the warehouses to be reloaded for the next batch of ships. Once inside the low level constant hum from the mooring beams dies out. This causes the ship builders, dockworkers and warehouse workers to stop what they are doing and move towards the windows and the main entrances.

Within minutes they all hear the low rumble of the engines on the vessels powering up. Soon afterwards a spray begins to rise from under the ships which increases shrouding them in a haze. Just as it looks like the ships would disappear, they begin to rise. As they do, in five separate warehouses cheers and applause can just be heard over the sound of these five vessels of human engineering and alien technologies taking off. Soon the cheers and applause died down and everyone returned to work they would have five new ships to look after in a very short while, and they still had much to get ready before the landed.

Meanwhile outside the docks and above the city of Atlantis the five ships of the Excelsior battle group slowly continue rising into the sky. Once above the city-ship, and more importantly above the shield perimeter of the city-ship, The Excelsior and her escort ships hover above Atlantis for a few minutes as the communicate with each other as well as Atlantis control. Soon the ships of the battle group turn to orient themselves all facing the same direction. Powerful hybridized computers reverse engineered from the Goa'uld, Alterran's, and the Asgard synchronize the maneuvers of the ships allowing them to move in near perfect precision.

Once facing the same direction the ships activated the powerful Gravitic Ion Engines of their main sublight drives. Pushing them away from the Ancient City, and once far enough away from the city they begin to pull themselves into orbit. Powerful shields and inertial compensators protect the crews and the ships from the forces exerted against them. All too soon the reach orbit, there along with the rest of the remaining ships of the Tau'ri fleet the Excelsior battle group waits for their final course out of the system from Atlantis. Comm. channels between the Excelsior and the rest of the fleet occur as the battle group waits for their final course out of the system and the nebula. Most of the comm's from the rest of the fleet to the battle group and her escorts is simple well wishes with a few good natured ribbing from the other ships of the fleet.

Within minutes the battle group receives their final course out of the system and the nebula and soon leaves the as yet un-named sanctuary planet behind. Once again the powerful engines of the Daedalus class and Prometheus sub-types push the ships toward the edge of the system and into the Nebula. There they activate a program Samantha Carter-O'Neill herself came up with many years ago on the original Prometheus during an encounter with a un known alien species in another nebula. The program allows the vessels hyperdrives to form a subspace bubble around the ships taking the ships partially into subspace with out fully entering hyperspace. This also has the side effect of allowing the ships to achieve a limited type of faster than light travel. Cutting their travel time through the nebula from days to mere hours. The reason they are traveling this way rather then going directly into hyperspace is a matter of security for the city-ship and refugees. Even though they are deep within the nebula and it is very unlikely the Wraith would detect the hyperspace window forming inside of it no-one wants to take that chance.

Hours latter the Excelsior and her battle group emerge from the nebula on the opposite side of the nebula facing Earth and where the Wraith is. Once on the edge of the nebula the powerful Asgard and Ancient based sensors of the ships scan the surrounding space making certain they are clear. Clear of any sign of the Wraith or any other observers the ships emerge from the nebula and disengage the program returning them to normal space. After several moments where the engineers check over the hybrid hyperdrive of the battle group making certain they are not damaged. Once cleared the Excelsior gives out the final course to the rest of her battle group, and once again their hyperspace generators are engaged this time to their full power. Soon after in front of each ship space begins to rent with the powerful forces being exerted against it. A blue and purple cloud appears in front of each ship for a few seconds looking like a storm in space. The scene does not last long however as the ships of the battle group shot into their respective clouds disappearing from the physical universe temporarily and into a deep layer of subspace. The clouds soon disappear in a flash leaving very little trace that anything at all happened.

**Wraith Controlled Earth**

**Wraith Hive**

**January 10, 2013 **

Pain. That is the first thing to come into his conscious mind deep aggravating pain. For five day's now since the Wraith conquered Earth and captured him alive they have tried to gain the secrets he buried deep in his mind. The first day he had spent in the company of the eldest Wraith Queen, yeah so not fun in his book. She had tried and failed to break him several times that day; fortunately for him he had experience in resisting that type of mental probing. The next several days the Wraith had spent beating him while the queen watched on again trying to break into his mental defenses. Again something he was unfortunately experienced at resisting and again so not fun. Right now he finds himself waking up in a kneeling position (so not good for his knees by the way) chained to a wall in a darkened dank and somewhat smelly cell. And the first thing he thinks to himself is how over the type clichéd they can get. He really wishes just for once some villain would try something new, he means seriously what do they do shop at villain's r'us or something. He even voices the thoughts out load knowing he is being monitored and not really caring.

He spends the next several minutes then explaining in excruciating detail exactly how and where they screwed up in not only there overall plan but in keeping him alive and detailing in detail what he plans to do to them once he escapes. And he will escape he believes it is just a question of when and how not if. He continues his diatribe for several minutes before the door to his cell opens and he has to shut his eyes to the light from outside the cell. He opens his eyes once the door is closed and see's the outline of a Wraith male standing before him. Before he can even begin with his usual glib insults and remarks the Wraith quickly crosses the distance between them forcing him to his feet. He scrunches his face and pain resisting the urge to make a noise even when the Wraith in question slams him into the wall. He opens his eyes and see's the Wraith in question right in his face his eyes going over his own face and head in great detail as if studying him. He feels the as the Wraith tries to worm his way into his mind again trying to break him.

After several minutes scrutinizing him the Wraith finally looks him in the eye and smiles. Oh this can't be good he thinks just before the Wraith says "Time to die, General."

The next thing he knows a hand is slapped to his chest and he feels a moment of invigoration just before excruciating pain shots through his body. He grits his teeth together as his face contorts due to the extreme pain it is a credit to the mans character that he is able to resist for as long as he does, but after a few minutes he opens his mouth and screams in pain and agony. Something he has only done twice in his life, once when he found his son dead and the other time when he was a prisoner of Ba'al. The last thought that crosses Jack O'Neill's mind before the darkness claims him as his life is being drained away is how much he wishes he could hold Sam in his arms one last time.


	2. Authurs Note

A/N

Just a Quick FYI for you all, First off I apologize this is not chapter 2, I am still working on Chapter 2, but unfortunately as usually does happen in these situations life has stepped in and sorta kicked me in the teeth a bit. So I am not as far along as I would like to be, But I will still be updating this story. I am just about finished my second scene, with only two more scene's planned for this chapter. On a positive note someone has offered to proof read the story for me, so I don't have to keep rewriting things as I go. Anyway I should hopefully have the chapter finished soon, but I am DEFIANTLY not putting a specific date and or time on it. I ask for your patience as I get the chapter done and posted. Thank you for reading and your note will be replaced by Chapter 2 when it is completed. And again Thank You.


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